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LiLinköping municipality has managed biogas driven buses in the regional transport system since 1997 and all buses in the municipality have run on biogas since 2015. Biogas is a renewable fuel and by replacing fossil fuels it can help to lower net CO2 emissions. However, Internal Combustion Engines (ICE) in buses still have a rather low efficiency, in the range of 15–30%. If the combustion of biogas instead takes place in a combined cycle gas turbine (CCGT) efficiency could be higher and heat losses reduced. This could be a feasible solution if the transport system instead used electric buses charged with electricity generated by the CCGT. This article has a top-down perspective on the regional transport system and the regional district heating system (DHS) in Linköping municipality. Two alternative systems are compared regarding CO2 emissions, electricity production and component efficiencies. The first system that is studied is in operation today and uses locally produced biogas in the ICE buses. In parallel the combined heat and power (CHP) system delivers electricity and heat to households in the region. The second system that is studied is a system with electric buses and a CHP system that uses biogas in the CCGT to deliver electricity and heat to the regional power grid and DHS. The study shows that emissions would be reduced if biogas use is changed from use in ICE buses to use in the CCGT in the CHP-DHS. Improved biogas use could lower CO2-eq emissions by 2.4 million kg annually by using a better fuel-energy pathway.